BioPerl is an active open source software project supported by the Open Bioinformatics Foundation.
BioPerl is a product of community effort to produce Perl code which is useful in biology.
BioPerl is a collection of Perl modules
It has played an integral role in the Human Genome Project
BioPerl is an active open source software project supported by the Open Bioinformatics Foundation.
BioPerl is a product of community effort to produce Perl code which is useful in biology.
BioPerl is a collection of Perl modules
It has played an integral role in the Human Genome Project
DevOps and Testing slides at DASA ConnectKari Kakkonen
My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
JMeter webinar - integration with InfluxDB and GrafanaRTTS
Watch this recorded webinar about real-time monitoring of application performance. See how to integrate Apache JMeter, the open-source leader in performance testing, with InfluxDB, the open-source time-series database, and Grafana, the open-source analytics and visualization application.
In this webinar, we will review the benefits of leveraging InfluxDB and Grafana when executing load tests and demonstrate how these tools are used to visualize performance metrics.
Length: 30 minutes
Session Overview
-------------------------------------------
During this webinar, we will cover the following topics while demonstrating the integrations of JMeter, InfluxDB and Grafana:
- What out-of-the-box solutions are available for real-time monitoring JMeter tests?
- What are the benefits of integrating InfluxDB and Grafana into the load testing stack?
- Which features are provided by Grafana?
- Demonstration of InfluxDB and Grafana using a practice web application
To view the webinar recording, go to:
https://www.rttsweb.com/jmeter-integration-webinar
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered QualityInflectra
In this insightful webinar, Inflectra explores how artificial intelligence (AI) is transforming software development and testing. Discover how AI-powered tools are revolutionizing every stage of the software development lifecycle (SDLC), from design and prototyping to testing, deployment, and monitoring.
Learn about:
• The Future of Testing: How AI is shifting testing towards verification, analysis, and higher-level skills, while reducing repetitive tasks.
• Test Automation: How AI-powered test case generation, optimization, and self-healing tests are making testing more efficient and effective.
• Visual Testing: Explore the emerging capabilities of AI in visual testing and how it's set to revolutionize UI verification.
• Inflectra's AI Solutions: See demonstrations of Inflectra's cutting-edge AI tools like the ChatGPT plugin and Azure Open AI platform, designed to streamline your testing process.
Whether you're a developer, tester, or QA professional, this webinar will give you valuable insights into how AI is shaping the future of software delivery.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
In this session I delve into the encryption technology used in Microsoft 365 and Microsoft Purview. Including the concepts of Customer Key and Double Key Encryption.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
DevOps and Testing slides at DASA ConnectKari Kakkonen
My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
JMeter webinar - integration with InfluxDB and GrafanaRTTS
Watch this recorded webinar about real-time monitoring of application performance. See how to integrate Apache JMeter, the open-source leader in performance testing, with InfluxDB, the open-source time-series database, and Grafana, the open-source analytics and visualization application.
In this webinar, we will review the benefits of leveraging InfluxDB and Grafana when executing load tests and demonstrate how these tools are used to visualize performance metrics.
Length: 30 minutes
Session Overview
-------------------------------------------
During this webinar, we will cover the following topics while demonstrating the integrations of JMeter, InfluxDB and Grafana:
- What out-of-the-box solutions are available for real-time monitoring JMeter tests?
- What are the benefits of integrating InfluxDB and Grafana into the load testing stack?
- Which features are provided by Grafana?
- Demonstration of InfluxDB and Grafana using a practice web application
To view the webinar recording, go to:
https://www.rttsweb.com/jmeter-integration-webinar
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered QualityInflectra
In this insightful webinar, Inflectra explores how artificial intelligence (AI) is transforming software development and testing. Discover how AI-powered tools are revolutionizing every stage of the software development lifecycle (SDLC), from design and prototyping to testing, deployment, and monitoring.
Learn about:
• The Future of Testing: How AI is shifting testing towards verification, analysis, and higher-level skills, while reducing repetitive tasks.
• Test Automation: How AI-powered test case generation, optimization, and self-healing tests are making testing more efficient and effective.
• Visual Testing: Explore the emerging capabilities of AI in visual testing and how it's set to revolutionize UI verification.
• Inflectra's AI Solutions: See demonstrations of Inflectra's cutting-edge AI tools like the ChatGPT plugin and Azure Open AI platform, designed to streamline your testing process.
Whether you're a developer, tester, or QA professional, this webinar will give you valuable insights into how AI is shaping the future of software delivery.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
In this session I delve into the encryption technology used in Microsoft 365 and Microsoft Purview. Including the concepts of Customer Key and Double Key Encryption.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on the notifications, alerts, and approval requests using Slack for Bonterra Impact Management. The solutions covered in this webinar can also be deployed for Microsoft Teams.
Interested in deploying notification automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 3. In this session, we will cover desktop automation along with UI automation.
Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
2. Why Talk About Bioperl?
• Successful open-source project
• Bioinformatics is a difficult field to
straddle
• Toolkit still has (many) flaws
• An evolving project
BOSC 2005
3. How Did We Get Here?
• A Brief History
• Development Stats
• People
• Bioperl in Action
BOSC 2005
4. Bioperl Development
Goals
• Provide a useable Perl toolkit for life
science data
• Solve problems that developers need
• Avoid the 1-off “everyone write a
BLAST|GenBank|FASTA parser”
• Continuity of solutions
BOSC 2005
5. A Brief History
2002
1997-1998 2000 Hackathons
AZ to ZA
Poster at ISMB 2004
Bio::SeqIO, Bio::DB
OMG Bio-Objects
“Core” Founded
bio.perl.org website Bioperl Bootcamp at UMontreal
EnsEMBL launched Bioperl 1.0 release
Bio::PreSeq bioperl-ext Bioperl paper
Bio::UnivAln BOSC2004
Gbrowse paper
Bio::Struct Bioperl 0.07
BLAST modules
HOWTOs started
BOSC2000 bioperl-run
Bioperl 0.01-0.04
BOSC2002
1999 2003
1996 2001 2005
Singapore Hackathon Bioperl 1.5 released
Ewan Birney becomes
VSNS-BCD bptutorial written
project leader after Steve Bioperl 1.2.3 released
Course Bioperl-db 100+ Paper references
Chervitz BioPipe paper published
Steven Brenner bioperl-db to have official
Bioperl 1.4 released
Steve Chervitz * BioCORBA release
Bio::SeqIO, Bio::Index
Chris Dagdigian BOSC2001 BOSC2005
bioperl-microarray
Richard Resnick
Releases 0.05-0.06 started
Lew Gramer
BioP BOSC2003
BioJava, BioPython
launched
Bioperl-99 mtg
BOSC 2005
6. Defining Points
• Vision of module(s) set by code owner
• She/He who writes it, “wins” argument
• Project leader/core developers
• can remove code before a release to
insure a working release
• Enforce code and module continuity
• Preserve API as much as possible
BOSC 2005
7. Project Mechanics
• Code is on a shared server (O|B|F)
• Publicly accessible
• Write-access to repository granted by
main developers
• Discussion of code, ideas on-list
BOSC 2005
11. Bioperl in Action
# Convert sequence formats
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format => ‘genbank’, -file=> ‘file.gbk’);
my $out = Bio::SeqIO->new(-format =>’fasta’,-file =>’>file.fas’);
while( my $seq = $in->next_seq ) {
$out->write_seq($seq);
}
----------------------------------
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => ‘blast’,
-file=> ‘result.blastp’);
while( my $r = $in->next_result ) {
while( my $h = $r->next_hit ) {
while( my $hsp = $h->next_hsp ) {
print $hsp->query->start, “..”,$hsp->query->end,”
”;
}
}
BOSC 2005
}
12. Bioperl in Action
# Convert sequence formats
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format => ‘embl’, -file=> ‘file.embl’);
my $out = Bio::SeqIO->new(-format =>’gcg’,-file =>’>file.gcg’);
while( my $seq = $in->next_seq ) {
$out->write_seq($seq);
}
----------------------------------
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => ‘fasta’,
-file => ‘result.fastp’);
while( my $r = $in->next_result ) {
while( my $h = $r->next_hit ) {
while( my $hsp = $h->next_hsp ) {
print $hsp->query->start, “..”,$hsp->query->end,”
”;
}
}
BOSC 2005
}
13. Measuring sucess
• 2002 Paper has 100+ Citations
• Bits and pieces used in many
informatics tools
• Bio::SearchIO (Rfam, In-Paranoid)
• Generic Genome Browser (Stein et
al, 2002)
• Comparative Genomics Library
(Yandell, Mungall, et al)
• [EnsEMBL]
BOSC 2005
14. Bioperl Taught At
Tutorials and Courses
CSHL Bioinformatics
Software Courses
Various mini courses
Bootcamp 2004
MIT, Duke, EBI, Pasteur
(Montreal)
BOSC 2005
15. Knowledge of Bioperl is
A Marketable Skill
http://bioag.byu.edu/botany/homepage/botweb/jobs_Ph.D.htm
Academic Facilities Coordinator II (Facilities)
http://www.ce.com/education/Bioinformatics-Certificate-
Bioinformatics Position at the UCR Genomics Institute
Program-10082109.htm
UC, Riverside
Track 1: Suggested electives for computer scientists and IT professionals
* Advanced Sequence Analysis in Bioinformatics (2 units)
The Center for Plant Cell Biology (CEPCEB) in the Genomics Institute of the University of California, Riverside,
* Gene Expression and Pathways (2 units)
invites applicants for an Academic Facilities Coordinator II position, an academic-track 11-month appointment.
* Protein Structure Analysis in Bioinformatics (2 units)
Salary for the position is commensurate with education and experience.
* Design and Implementation of Bioinformatics Infrastructures (3 units)
* DNA Microarrays - Principles, Applications and Data Analysis (2 Units)
The successful applicant will be expected to organize a small bioinformatics team to provide support to The Center
* Parallel and Distributed Computing for Bioinformatics (2 units)
for Plant Cell Biology. This team will implement currently available bioinformatics tools including relational database
Track 2: Suggested electives for molecular biologists and other scientists
support and will develop user-specific data-mining tools. The appointee will be expected to develop research
* Introduction to Programming for Bioinformatics II*** (3 units)
collaborations with the faculty and teach or organize short courses that will inform that will inform the local
* Introduction to Programming for Bioinformatics III (3 units)
community about the available bioinformatics resources. Applicants must have a Ph.D. in the Biological Sciences
BioPerl for Bioinformatics (2 units)
* (Plant Biology is preferred). Applicants with experience in leading a bioinformatics group will be given preference.
* Design and Implementation of Bioinformatics Infrastructures (3 units) Additionally, the applicant must be proficient in one or more programming languages (PERL, PYTHON, JAVA, C++)
* Gene Expression and Pathways (2 units) and have a good understanding of database design and implementation. In addition, applicants should have
* Protein Structure Analysis in Bioinformatics (2 units) experience using one of the open source bioinformatics frameworks such as BIOJAVA or
* DNA Microarrays - Principles, Applications and Data Analysis (2 units)
BIOPERL. The applicant should have experience with software collaboration tools such as CVS. The applicant
will be expected to oversee the purchase, installation, and management of the necessary computer hardware and
http://www.foothill.fhda.edu/bio/programs/bioinfo/curric.shtml software required to provide bioinformatics support to several users. A good understanding of the UNIX operating
system and systems administration is also an important qualification.
CAREER CERTIFICATE REQUIREMENTS (49 units)*
http://careers.psgs.com/CareerOppLocation2.asp?location=BETHESDA
Biotechnology Core Courses (14 units) CF-046: Bioinformatics Specialist
BTEC 51A Cell Biology for Biotechnology (3 units)
BTEC 52A Molecular Biology for Biotechnology (3 units) The NIAID Office of Technology and Information Systems (OTIS)/Bioinformatics and Scientific IT Program (BSIP) is seek-ing
BTEC 65 DNA Electrophoretic Systems (1 unit) a bioinformatics specialist. The position includes managing our bioinformatics services and applications, training NIH
BTEC 68 Polymerase Chain Reaction (1 unit) scientists, creating and modifying simple bioinformatics software, and collaborating with NIH scientists on specific projects.
BTEC 71 DNA Sequencing & Bioinformatics (1 unit) [snip]
BTEC 76 Introduction to Microarray Data Analysis (2 unit)
BTEC 64 Protein Electrophoretic Systems (1 unit) The qualified candidate must hold a Master's Degree (or equivalent) and three years of experience or a Ph. D in life science
BTEC 66 HPLC (2 units) or computer science. The candidate must have strong interpersonal, written and oral communication skills and be a lateral
thinker. Must be able to communicate current bioinformatics technology in a clear and precise manner and to discuss
Computer Science Core Courses (30 units) projects with scientists and advise what relevant tools may be used or implemented, have the ability to locate relevant data/
CIS 52A Introduction to Data Management Systems (5 units) information and put this into the context of projects they work on. Candidate must have expert knowledge of UNIX (Mac OS
CIS 52B2 Introduction to Oracle SQL (5 units) X Darwin a plus), with the ability to install and configure command-line-based applications and services. These include: UNIX
CIS 68A Introduction to UNIX (5 units)
windowing systems (X11, FreeX86), UNIX-based open source scientific applications, Perl and BioPerl scripts,
CIS 68E Introduction to PERL (5 units)
HTML, XML. Must have experience with one or more of the following: · Web services (WSDL, SOAP) · Genomics and
CIS 68H Introduction to BioPerl (5 units) proteomics · Protein structure prediction/visualization. · Sequence analysis, alignment and database searches. · Regular
BOSC 2005
COIN81 Bioinformatics Tools & Databases (5 units) expressions and relational database queries. · Data mining, text mining · Biostatistics
16. Why has the Project
Worked?
• A critical mass of individuals who
wanted to solve a common problem
• Infrastructure that works
• Sense of community
• Sharing information, tutorials
BOSC 2005
17. Some Key Developers
Not Pictured
Richard Adams
Scott Cain
Sean Davis
Stefan Kirov
Nathan Haigh
Marc Logghe
Chad
Heikki Aaron Steve Jason Shawn Allen
Ewan Chris M Hilmar Lincoln Brian Chris D
BOSC 2005
18. Infrastructure
• Easily accessible CVS, web service
• Reliable
• Machines that we own
• Additional services can be added
• Moving to faster machines this summer
BOSC 2005
19. Collaborative Nature
of the Project
• Folks working on similar problems
• Pooled development resources
• Friendly & interactive way to do
science
• Shared user support load...
BOSC 2005
20. Open Source is Good!
• Fix things faster
• (If you really care about the fix)
• Everyone can see solution, audit code
• Contribution can be modular
• “Give a little, get a lot”
• More developers for less resources
BOSC 2005
21. Open Source Doesn’t
Solve Everything
• Best laid plans
• Decision by consensus ...
• ... Free-for-all committing
• Things don’t “just happen”
• Need strong leadership, vision, and
commitment
• Documentation tends to lag
• Interesting, needed code trumps boring
BOSC 2005
22. Great Power ==
Great Responsibility
• Making releases
• Point releases maintain API
• Attempt to maintain backwards
compatibility between stable releases
• Many people depend on the code
• Additional modules should maintain
continuity
BOSC 2005
24. Bioperl: Present Day
• Parsers for
• Sequence & alignment parsing
• Gene Prediction output
• Phylogenetic trees
• Weight Matricies (TFBS)
• Ontologies
• Structure data
• Various CompBio, MolEvol apps
BOSC 2005
25. Bioperl: Present Day
• Tools for
• Sequence manipulation (I/O, manip)
• Graphical sequence rendering
• Sequence & alignment stats, popgen
tests, molevo tests
• Access to Local & Remote Sequence
Databases
BOSC 2005
26. Present Day Stats
• 780+ modules
• 336,000 lines of code
• ~9,000 tests in unit test ‘t’ dir
• 57 utility scripts, 60 example scripts
• 11 HOWTO docs
• 44 Q&A in FAQ
BOSC 2005
27. Bioperl Magic
• Using interfaces to hide specifics
• Bio::DB::GenBank & Bio::Index::GenBank
• Objects can masquerade like other objects
• Bio::SeqFeature::Generic, Bio::Location,
DB::GFF::RelSegment, DB::GFF::Feature
BOSC 2005
28. Bioperl Magic
use Bio::DB::GenBank;
use Bio::DB::Fasta;
my $db = Bio::DB::GenBank->new;
my $idx = Bio::DB::Fasta->new($fafile_dir);
my $seq1 = $db->get_Seq_by_acc($acc);
my $seq2 = $idx->get_Seq_by_acc($acc);
use Bio::DB::FileCache;
my $cachedb = Bio::DB::FileCache->new($db);
my $acc = $cachedb->get_Seq_by_acc($acc);
BOSC 2005
29. ...The Problems
• Interfaces system is cluttered
• Learning curve is steep
• Nonsensical to some people
• OO Code is too slow
• Developer community needs growth
BOSC 2005
30. Why is Bioperl Slow
(in some places)?
1. Object-Oriented Perl is a Hack!
1. $class->SUPER::new(@_);
2. $class->SUPER::_rearrange(@_);
3. Object overhead can be high.
BOSC 2005
31. Research with Bioperl
• Genome annotation pipeline
• Genome Browsing
• Comparative genomics
• Phylogenomics
BOSC 2005
32. S.cerevisiae
Existing Genome C.glabrata
Annotation K.lactis
New K.waltii
Annotation A.gossypii
D.hansenii
C.guilliermondii
C.lusitaniae
Hemiascomycota
Y.lipolytica
P.anserina
C.globsum
N.crassa
M.grisea
Euascomycota F.graminearum
A.fumigatus
A.nidulans
H.capsulatum
C.immitis
Archiascomycota S.pombe
C.cinereus
P.chrysosporium
Basidiomycota C.neoformans
U.maydis
Zygomycota R.oryzae
H.sapiens
Protein ML tree based on 100 random orthologs
A.thaliana
10
33. Genome Annotation
Pipeline
Rfam
tRNAscan
ZFF to GFF3 GFF to AA
SNAP FASTA
predicted
Proteins
proteins
Twinscan all-vs-all
GFF2 to GFF3
Bio::DB::GFF
Tools::Glimmer
Glimmer SearchIO
protein to
Genscan
Genome genome
Tools::Genscan
coordinates
homologs
HMMER MCL
SearchIO SearchIO and
BLASTZ
orthologs
BLASTN
Tools::GFF GLEAN
GFF2 to GFF3
exonerate (combiner)
Proteins Gene
protein2genome
families
exonerate
ESTs
est2genome
BOSC 2005
39. Where Should Bioperl
be Headed?
• Concise set of functionality that just
works?
• Supporting leading edge of research?
• Beginner level tools?
• Advanced tools?
BOSC 2005
40. Challenges
• Logistics
• Building and maintaining large
projects takes a lot of time
• Project leaders with vision (and time)
• Face-to-face time invaluable for
coordination
• Need more dedicated developers
BOSC 2005
41. Starting Over?
• Years of organic development don’t
make a wholly consistent toolkit
• Keeping POD up to date vs API
maintenance
• Autodoc-ing?
• Perl6 rewrite?
• Do we start a Bioperl 2, from scratch?
BOSC 2005
42. Supporting the Toolkit
• Consider applying for funding to
support a developer?
• Finding companies to provide more
dedicated user support?
• Gatherings (hackathons)
• DocFests to increase documentation
• Better incentives for bug fixes
BOSC 2005
43. My Priority Queue
• Simplified API, hidden interfaces
• Overview docs point functionality to
modules
• Speed
• Extensibility
BOSC 2005
44. A Plan
• Continue Bioperl 1.x
• Try and fix interface overload
• Work out speed issues (maybe)
• Encourage dabbling into a 2.0 codebase
• Outline some key principals in new
codebase.
• Consider prototypes & Perl6
BOSC 2005
45. We’ve Grown Up
• Over the course of the project we have
• Gotten married
• Had kids
• Changed continents
• Changed jobs
BOSC 2005